Browsing by Author "Long, Eric C."
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Item Advances in Solid Phase Microextraction for the Analysis of Volatile Compounds in Explosives, Tire Treatments, and Entomological Specimens(2016-05) Kranz, William D.; Goodpaster, John V.; Manicke, Nick; Sardar, Rajesh; Picard, Christine Johanna; Long, Eric C.Solid phase micro-extraction is a powerful and versatile technique, well-suited to the analysis of numerous samples of forensic interest. The exceptional sensitivity of the SPME platform, combined with its adaptability to traditional GC-MS systems and its ability to extract samples with minimal work-up, make it appropriate to applications in forensic laboratories. In a series of research projects, solid phase micro-extraction was employed for the analysis of explosives, commercial tire treatments, and entomological specimens. In the first project, the volatile organic compounds emanating from two brands of pseudo-explosive training aids for use in detector dog imprinting were determined by SPME-GC-MS, and the efficacy of these training materials was tested in live canine trials. In the second project, the headspace above various plasticizers was analyzed comparative to that of Composition C-4 in order to draw conclusions about the odor compound, 2- ethyl-1-hexnaol, with an eye toward the design of future training aids. In the third, automobile tires which had participated in professional race events were analyzed for the presence of illicit tire treatments, and in the fourth, a novel SPME-GC-MS method was developed for the analysis of blowfly (Diptera) liquid extracts. In the fifth and final project, the new method was put to the task of performing a chemotaxonomic analysis on pupa specimens, seeking to chemically characterize them according to their age, generation, and species.Item Advancing the Applicability of Fast Photochemical Oxidation of Proteins to Complex Systems(2016-08) Rinas, Aimee Lynn; Jones, Lisa; Georgiadis, Millie M.; Long, Eric C.; Manicke, NicholasHydroxyl radical protein footprinting coupled with mass spectrometry has become an invaluable technique for protein structural characterization. In this method, hydroxyl radicals react with solvent exposed amino acid side chains producing stable, covalently attached labels. Although this technique yields beneficial information, the extensive list of known oxidation products produced increases the complexity of identifying and quantifying oxidation products. The current methods available for quantifying the extent of oxidation either involve manual analysis steps, or limit the number of searchable modifications or the size of sequence database. This creates a bottleneck which can result in a long and arduous analysis process, which is further compounded in a complex sample. In addition to the data complexity, the peptides containing the oxidation products of hydroxyl radical-mediated protein footprinting experiments are typically much less abundant than their unoxidized counterparts. This is inherent to the design of the experiment as excessive oxidation may lead to undesired conformational changes or unfolding of the protein, skewing the results. Thus, as the complexity of the systems studied using this method expands, the detection and identification of these oxidized species can be increasingly difficult with the limitations of data-dependent acquisition (DDA) and one-dimensional chromatography. The recently published in cell FPOP method exemplifies where this field is headed - larger and more complex systems. This dissertation describes two new methodologies and one new technology for hydroxyl radical-mediated protein footprinting, expanding the applicability of the method. First is development of a new footprinting analysis method for both peptide and residue level analysis, allowing for faster quantification of results. This method utilizes a customized multilevel search workflow developed for an on-market search platform in conjunction with a quantitation platform developed using a free Excel add-in, expediting the analysis process. Second is the application of multidimensional protein identification technology (MudPIT) in combination with hydroxyl radical footprinting as a method to increase the identification of quantifiable peptides in these experiments. Last is the design and implementation of a flow system for in cell FPOP, which hydrodynamically focuses the cells, and when used yielded a 13-fold increase in oxidized proteins and 2 orders of magnitude increase in the dynamic range of the method.Item Combination therapy in a xenograft model of glioblastoma: enhancement of the antitumor activity of temozolomide by an MDM2 antagonist(American Association of Neurological Surgeons, 2017-02) Wang, Haiyan; Cai, Shanbao; Bailey, Barbara J.; Saadatzadeh, M. Reza; Ding, Jixin; Tonsing-Carter, Eva; Georgiadis, Taxiarchis M.; Gunter, T. Zachary; Long, Eric C.; Minto, Robert E.; Gordon, Kevin R.; Sen, Stephanie E.; Cai, Wenjing; Eitel, Jacob A.; Waning, David L.; Bringman, Lauren R.; Wells, Clark D.; Murray, Mary E.; Sarkaria, Jann N.; Gelbert, Lawrence M.; Jones, David R.; Cohen-Gadol, Aaron A.; Mayo, Lindsey D.; Shannon, Harlan E.; Pollok, Karen E.; Pediatrics, School of MedicineOBJECTIVE Improvement in treatment outcome for patients with glioblastoma multiforme (GBM) requires a multifaceted approach due to dysregulation of numerous signaling pathways. The murine double minute 2 (MDM2) protein may fulfill this requirement because it is involved in the regulation of growth, survival, and invasion. The objective of this study was to investigate the impact of modulating MDM2 function in combination with front-line temozolomide (TMZ) therapy in GBM. METHODS The combination of TMZ with the MDM2 protein-protein interaction inhibitor nutlin3a was evaluated for effects on cell growth, p53 pathway activation, expression of DNA repair proteins, and invasive properties. In vivo efficacy was assessed in xenograft models of human GBM. RESULTS In combination, TMZ/nutlin3a was additive to synergistic in decreasing growth of wild-type p53 GBM cells. Pharmacodynamic studies demonstrated that inhibition of cell growth following exposure to TMZ/nutlin3a correlated with: 1) activation of the p53 pathway, 2) downregulation of DNA repair proteins, 3) persistence of DNA damage, and 4) decreased invasion. Pharmacokinetic studies indicated that nutlin3a was detected in human intracranial tumor xenografts. To assess therapeutic potential, efficacy studies were conducted in a xenograft model of intracranial GBM by using GBM cells derived from a recurrent wild-type p53 GBM that is highly TMZ resistant (GBM10). Three 5-day cycles of TMZ/nutlin3a resulted in a significant increase in the survival of mice with GBM10 intracranial tumors compared with single-agent therapy. CONCLUSIONS Modulation of MDM2/p53-associated signaling pathways is a novel approach for decreasing TMZ resistance in GBM. To the authors' knowledge, this is the first study in a humanized intracranial patient-derived xenograft model to demonstrate the efficacy of combining front-line TMZ therapy and an inhibitor of MDM2 protein-protein interactions.Item Combining Semiempirical QM Methods with Atom Dipole Interaction Model for Accurate and Efficient Polarizability Calculations(2022-12) Young, Ryan; Pu, Jingzhi; Long, Eric C.; Naumann, Christoph; Sardar, RajeshMolecular polarizability plays a significant role in chemistry, biology, and medicine. Classical prediction of polarizability often relies on atomic-type specific polarizability optimized for training set molecules, which limits the calculations to systems of similar chemical environment. Although ab initio (AI) quantum mechanical (QM) methods are more transferable in predicting molecular polarizability, their high computational costs especially when used with large basis sets for obtaining quantitatively reliable results make them less practical. To obtain accurate QM polarizability in an efficient manner, we have developed a dual-level approach, where the polarizability (α) obtained from the efficient semiempirical QM (SE) method is corrected using a set of element-base atomic polarizabilities derived from the atomic dipole interaction model (ADIM) to reproduce the density functional theory (DFT) results. We have optimized the atomic polarizability correction parameters for CHON-containing systems using a small training set of molecules and tested the resulting SE-ADIM model on the neutral drug-like molecules in the QM7B database. SE-ADIM corrected AM1 showed substantial improvement with its relative percent error (RPE) compared to B3LYP reduced from 33.81% to 3.35%. To further test its robustness for larger molecules in broader chemical bonding situations, we applied this method to a collection of drug molecules from the e-Drug3D database. For the 1004 molecules tested, our SE-ADIM model, which only contains four empirical parameters, greatly reduces the RPE in AM1 polarizability relative to B3LYP from 26.8% to 2.9%. Error decomposition shows consistent improvements across molecules with diverse bond saturations, molecular sizes, and charge states. In addition, we have applied AlphaML, a promising machine learning (ML) technique for predicting molecular polarizability, to the e-Drug3D dataset to compare its performance with our SE-ADIM correction of AM1. We found SE-ADIM performs competitively with AlphaML bolstering our confidence in the value of our method. Errors distinct to AlphaML were also discovered. We found four molecules for which AlphaML predicts negative molecular polarizabilities, all of which were peroxides. In contrast, SE-ADIM has no such issue with these molecules or this chemical type. Finally, to improve performance of SE-ADIM when correcting AM1 molecular polarizability calculations for charged molecules, we introduce a charge dependent polarizability (CDP) enabled SE-ADIM. Training the CDP enabled SE-ADIM with a single additional parameter, B, we were able to reduce error in AM1 molecular polarizability calculations of charged molecules relative to B3LYP from 29.57% to 5.16%. By contrast, SE-ADIM without CDP corrected AM1 relative to B3LYP had an RPE of 8.56%. The most benefit of CDP was evident within negatively charged molecules where AM1 error relative to B3LYP fell from 32.20% to 3.77% while SE-ADIM without CDP enabled error for these same negative molecules was 10.06%.Item A comparison of first-semester organic chemistry students' experiences and mastery of curved-arrow formalism in face-to-face and cyber peer-led team learning(2015-12-03) Wilson, Sarah Beth; Varma-Nelson, Pratibha; Bodner, George; Anderson, Trevor; Bodner, Robert; Long, Eric C.The cyber Peer-Led Team Learning (cPLTL) workshops are a synchronous online adaptation of the educational intervention PLTL, in which students, under the guidance of undergraduate peer facilitators, collaboratively solve problems in small groups. The purpose of this parallel convergent mixed methods study was to assess the impact of implementing cPLTL in an organic chemistry course on students’ workshop experiences, performance, and development of curved-arrow formalism skills. Statistical analyses revealed comparable attendance rates, distribution of course grades, and achievement on American Chemical Society First-semester Organic Chemistry Exams. However, plotting workshop grades by AB, C, and DFW grade groupings revealed that PLTL students earned more successful grades than their cPLTL counterparts (91% vs 77% ABC grades). Utilization of a new curved-arrow formalism analytic framework for coding student interview artifacts revealed that cPLTL students were statistically less likely to successfully draw the product suggested by the curved-arrows than their PLTL classmates. Both PLTL and cPLTL students exhibited a comparable incidence of relational to instrumental learning approaches. Similarly, both PLTL and cPLTL students were more likely to exhibit a common Scheme for Problem-Solving in Organic Chemistry (SPOC) than having dialogue that could be characterized by Toulmin’s Argumentation scheme. Lastly, implications for faculty are suggested, including: developing more explicit connections concept, mode, and reasoning components of understanding curved-arrow formalism for organic chemistry students; optimizing graphical collaborative learning activities for online learners; and developing online students’ sense of community.Item Development of Total Vaporization Solid Phase Microextraction and Its Application to Explosives and Automotive Racing(2015) Bors, Dana E.; Goodpaster, John V.; Picard, Christine Johanna; Shepson, Paul; Cooks, Graham; Long, Eric C.Pipe bombs are a common form of improvised explosive device, due in part to their ease of construction. Despite their simplistic nature, the lethality of pipe bombs should not be dismissed. Due to the risk of harm and their commonality, research into the pipe bomb deflagration process and subsequent chemical analysis is necessary. The laboratory examination of pipe bomb fragments begins with a visual examination. While this is presumptive in nature, hypotheses formed here can lead to subsequent confirmatory exams. The purpose of this study was to measure the mass and velocity of pipe bomb fragments using high speed video. These values were used to discern any trends in container type (PVC or black/galvanized steel), energetic filler (Pyrodex or double base smokeless powder), and ambient temperature (13°C and -8°C). The results show patterns based on container type, energetic filler, and temperature. The second stage of a laboratory exam is chemical analysis to identify any explosive that may be present. Legality calls for identification only, not quantitation. The purpose of this study is to quantitate the amount of explosive residue on post-blast pipe bomb fragments. By doing so, the instrumental sensitivities required for this type of analysis will be known. Additionally, a distribution of the residue will be mapped to provide insight into the deflagration process of a device. This project used a novel sampling technique called total vaporization solid phase microextraction. The method was optimized for nitroglycerin, the main energetic in double base smokeless powder. Detection limits are in the part per billion range. Results show that the concentration of residue is not uniform, and the highest concentration is located on the endcaps regardless of container type. Total vaporization solid phase microextraction was also applied to automotive racing samples of interest to the National Hot Rod Association. The purpose of this project is two-fold; safety of the race teams in the form of dragstrip adhesive consistency and monitoring in the form of fuel testing for illegal adulteration. A suite of analyses, including gas chromatography mass spectrometry, infrared spectroscopy, and evaporation rate, were developed for the testing of dragstrip adhesives. Gas chromatography mass spectrometry methods were developed for both nitromethane based fuel as well as racing gasolines. Analyses of fuel from post-race cars were able to detect evidence of adulteration. Not only was a novel technique developed and optimized, but it was successfully implemented in the analysis of two different analytes, explosive residue and racing gasoline. TV-SPME shows tremendous promise for the future in its ability to analyze a broad spectrum of analytes.Item DNA Cleaving "Tandem-Array" Metallopeptides Activated With KHSO5: Towards the Development of Multi-Metallated Bioactive Conjugates and Compounds(Bentham Science, 2014) Lewis, Mark A.; Williams, Katie M.; Fang, Ya-Yin; Schultz, Franklin A.; Long, Eric C.; Department of Chemistry and Chemical Biology, School of ScienceAmino terminal peptides of the general form Gly-Gly-His have been used to introduce single sites of metal binding and redox activity into a wide range of biomolecules to create bioactive compounds and conjugates capable of substrate oxidation. We report here that Gly-Gly-His-like peptides linked in a tandem fashion can also be generated leading to multi-metal binding arrays. While metal binding by the native Gly-Gly-His motif (typically to Cu(2+), Ni(2+), or Co(2+)) requires a terminal peptide amine ligand, previous work has demonstrated that an ornithine (Orn) residue can be substituted for the terminal Gly residue to allow solid-phase peptide synthesis to continue via the side chain N-δ. This strategy thus frees the Orn residue N-α for metal binding and permits placement of a Gly-Gly-His-like metal binding domain at any location within a linear, synthetic peptide chain. As we show here, this strategy also permits the assembly of tandem arrays of metal binding units in linear peptides of the form: NH2-Gly-Gly-His-[(δ)-Orn-Gly-His]n-(δ)-Orn-Gly-His-CONH2 (where n = 0, 1, and 2). Metal binding titrations of these tandem arrays monitored by UV-vis and ESI-MS indicated that they bind Cu(2+), Ni(2+), or Co(2+) at each available metal binding site. Further, it was found that these systems retained their ability to modify DNA oxidatively and to an extent greater than their parent M(II)•Gly-Gly-His. These findings suggest that the tandem array metallopeptides described here may function with increased efficiency as "next generation" appendages in the design of bioactive compounds and conjugates.Item DNA Targeting as a Likely Mechanism Underlying the Antibacterial Activity of Synthetic Bis-Indole Antibiotics(American Society for Microbiology, 2016-11-21) Opperman, Timothy J.; Kwasny, Steven M.; Bo Li, Jessica; Lewis, Mark A.; Aiello, Daniel; Williams, John D.; Peet, Norton P.; Moir, Donald T.; Bowlin, Terry L.; Long, Eric C.; Chemistry and Chemical Biology, School of ScienceWe previously reported the synthesis and biological activity of a series of cationic bis-indoles with potent, broad-spectrum antibacterial properties. Here, we describe mechanism of action studies to test the hypothesis that these compounds bind to DNA and that this target plays an important role in their antibacterial outcome. The results reported here indicate that the bis-indoles bind selectively to DNA at A/T-rich sites, which is correlated with the inhibition of DNA and RNA synthesis in representative Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) organisms. Further, exposure of E. coli and S. aureus to representative bis-indoles resulted in induction of the DNA damage-inducible SOS response. In addition, the bis-indoles were found to be potent inhibitors of cell wall biosynthesis; however, they do not induce the cell wall stress stimulon in S. aureus, suggesting that this pathway is inhibited by an indirect mechanism. In light of these findings, the most likely basis for the observed activities of these compounds is their ability to bind to the minor groove of DNA, resulting in the inhibition of DNA and RNA synthesis and other secondary effects.Item IUPUI Imaging Research Council(Office of the Vice Chancellor for Research, 2012-04-13) Hutchins, Gary D.; Wilson, Kathryn J.; Sturek, Michael S.; Du, Eliza Y.; Fletcher, James W.; Long, Eric C.; Molitoris, Bruce A.; Johnson, Daniel P.; Day, Richard N.; Barnett, William K.; Palakal, Mathew J.Abstract The IUPUI Imaging Research Council was created by the IUPUI Vice Chancellor for Research to provide guidance and direction for expansion of research imaging initiatives across all Schools and Departments within IUPUI. The specific goals of the council are: • To encourage and coordinate collaboration among IUPUI researchers from different disciplines • To provide advice and guidance in the realization of highly competitive large grant proposals that will support and grow the IUPUI imaging efforts into major nationally and internationally recognized programs • To develop a strategic plan that will enable IUPUI to become nationally and internationally known as the place for imaging research and its applications • To determine strategic areas of strength and growth • To determine available and needed resources • To determine strategic external partnerships Activities organized by the council to date include sponsoring an IUPUI Imaging Research Workshop on November 17, 2011. This workshop consisted of invited presentations, a poster session, and working group breakout sessions. Working groups explored research opportunities and needs in four priority areas (neuroscience, cancer, cardiovascular disease, and remote sensing). The council has recently initiated a monthly seminar series and is actively developing an IUPUI research imaging strategic plan. For more information visit the IUPUI Imaging Research Initiative website at www.imaging.iupui.edu.Item Potentiation of Carboplatin-Mediated DNA Damage by the Mdm2 Modulator Nutlin-3a in a Humanized Orthotopic Breast-to-Lung Metastatic Model(American Association for Cancer Research, 2015-12) Tonsing-Carter, Eva; Bailey, Barbara J.; Saadatzadeh, M. Reza; Ding, Jixin; Wang, Haiyan; Sinn, Anthony L.; Peterman, Kacie M.; Spragins, Tiaishia K.; Silver, Jayne M.; Sprouse, Alyssa A.; Georgiadis, Taxiarchis M.; Gunter, T. Zachary; Long, Eric C.; Minto, Robert E.; Marchal, Christophe C.; Batuello, Christopher N.; Safa, Ahmad R.; Hanenberg, Helmut; Territo, Paul R.; Sandusky, George E.; Mayo, Lindsey D.; Eischen, Christine M.; Shannon, Harlan E.; Pollok, Karen E.; Department of Pharmacology and Toxicology, IU School of MedicineTriple-negative breast cancers (TNBC) are typically resistant to treatment, and strategies that build upon frontline therapy are needed. Targeting the murine double minute 2 (Mdm2) protein is an attractive approach, as Mdm2 levels are elevated in many therapy-refractive breast cancers. The Mdm2 protein-protein interaction inhibitor Nutlin-3a blocks the binding of Mdm2 to key signaling molecules such as p53 and p73α and can result in activation of cell death signaling pathways. In the present study, the therapeutic potential of carboplatin and Nutlin-3a to treat TNBC was investigated, as carboplatin is under evaluation in clinical trials for TNBC. In mutant p53 TMD231 TNBC cells, carboplatin and Nutlin-3a led to increased Mdm2 and was strongly synergistic in promoting cell death in vitro. Furthermore, sensitivity of TNBC cells to combination treatment was dependent on p73α. Following combination treatment, γH2AX increased and Mdm2 localized to a larger degree to chromatin compared with single-agent treatment, consistent with previous observations that Mdm2 binds to the Mre11/Rad50/Nbs1 complex associated with DNA and inhibits the DNA damage response. In vivo efficacy studies were conducted in the TMD231 orthotopic mammary fat pad model in NOD.Cg-Prkdc(scid)Il2rg(tm1Wjl)/SzJ (NSG) mice. Using an intermittent dosing schedule of combined carboplatin and Nutlin-3a, there was a significant reduction in primary tumor growth and lung metastases compared with vehicle and single-agent treatments. In addition, there was minimal toxicity to the bone marrow and normal tissues. These studies demonstrate that Mdm2 holds promise as a therapeutic target in combination with conventional therapy and may lead to new clinical therapies for TNBC.